Shaw is prejudice against humans not other mutants. I think Shaw being a arrogent hypocrite thinks his above human issues like that. He didn't care about working with Soviets, Nazis or the U.S or their ideology his only intrest was in creating his own post apocalyptic mutant empire

Your right. Earlier in the movie in fact he states how a person's apperance doesn't make them the ultimate race (blonde hair and blue eyes? Pathetic.) But the fact that they're the next stage in human evolution does.